rs262929

Variant names:

• chr6-37176628-A-G
• rs262929
• ENST00000732913.1:n.31+1141A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-37176628-A-G
• chr6-37176628-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000732913.1(ENSG00000295829):​n.31+1141A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.804 in 152,120 control chromosomes in the GnomAD database, including 49,293 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.80 (49293 hom., cov: 32)
• Consequence: ENSG00000295829 ENST00000732913.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 2 publications found

Genes affected

ENSG00000295829 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000732913.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295829	ENST00000732913.1		n.31+1141A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.804 AC: 122165 AN: 152002 Hom.: 49236 Cov.: 32

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.876

Gnomad SAS AF: 0.884

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.799

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.804 AC: 122282 AN: 152120 Hom.: 49293 Cov.: 32 AF XY: 0.805 AC XY: 59823 AN XY: 74358

African (AFR) AF: 0.806 AC: 33459 AN: 41494

American (AMR) AF: 0.830 AC: 12683 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.800 AC: 2775 AN: 3468

East Asian (EAS) AF: 0.876 AC: 4542 AN: 5184

South Asian (SAS) AF: 0.883 AC: 4258 AN: 4822

European-Finnish (FIN) AF: 0.752 AC: 7946 AN: 10570

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.794 AC: 53952 AN: 67986

Other (OTH) AF: 0.798 AC: 1686 AN: 2114

Alfa AF: 0.798 Hom.: 72910

Bravo AF: 0.808

Asia WGS AF: 0.875 AC: 3043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.42
DANN	Benign	0.14
PhyloP100		-1.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs262929; hg19: chr6-37144404;